SMED30030473

Overview
NameSMED30030473
Smed IDSMED30030473
Length (bp)1165
Neoblast Clusters

Zeng et. al., 2018



 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30030473

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30030473SMESG000070523.1 Contig35151newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30030473SMESG000070523.1 Contig35151uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030473 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012087:10316..15956 -5779
v31.021310:1400..7045 -5670
Homology
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BLAST of SMED30030473 vs. Planmine SMEST
Match: SMESG000070523.1 (SMESG000070523.1)

HSP 1 Score: 411.764 bits (1057), Expect = 1.784e-141
Identity = 215/216 (99.54%), Postives = 216/216 (100.00%), Query Frame = 1 
Query:  232 VTMNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKXXXXXXXXXXXXXXVTNFHKEITIMFETKREVIITEKDFTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNIIWLELMYICFVLPFYGMFFVILEIRKHKAVISIDKRRKATKYRNLNDLMRQCSRPLDNSQILQDKYGKLNLYQYSSSDK 879
            +TMNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKLIGSLLNLINSNLNVTNFHKEITIMFETKREVIITEKDFTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNIIWLELMYICFVLPFYGMFFVILEIRKHKAVISIDKRRKATKYRNLNDLMRQCSRPLDNSQILQDKYGKLNLYQYSSSDK
Sbjct:  270 MTMNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKLIGSLLNLINSNLNVTNFHKEITIMFETKREVIITEKDFTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNIIWLELMYICFVLPFYGMFFVILEIRKHKAVISIDKRRKATKYRNLNDLMRQCSRPLDNSQILQDKYGKLNLYQYSSSDK 485
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BLAST of SMED30030473 vs. Planmine SMEST
Match: SMESG000070513.1 (SMESG000070513.1)

HSP 1 Score: 247.284 bits (630), Expect = 4.747e-77
Identity = 133/213 (62.44%), Postives = 164/213 (77.00%), Query Frame = 1 
Query:  238 MNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKXXXXXXXXXXXXXXVTNFHKEITIMFETKREVIITEKDFTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNIIWLELMYICFVLPFYGMFFVILEIRKHKAVISIDKRRKATKYRNLNDLMRQCSRPLDNSQILQDKYGKLNLYQYSSSD 876
            MNFYCIMPFYPT GSVIIFAHNGYP DETYY L LF+NNEEVSFSSQ YI+IPY+ VG K+ LIG LLNLIN NLNVTN +KEI IMFET++EVII+ +DFTCADL+N E+ YHQLSK +L+FYAE+H L +   IW E + +  +LP Y +  +I+EI KHK+  +I  RRKATK+R LNDL+   S+   N + L+ ++ K NLY  SS+D
Sbjct:  303 MNFYCIMPFYPTRGSVIIFAHNGYPSDETYYTLSLFNNNEEVSFSSQQYIKIPYDTVGRKVVLIGKLLNLINPNLNVTNIYKEIWIMFETEKEVIISPRDFTCADLSNLEIRYHQLSKTTLLFYAEIHHLAIHYFIWTEFLCVLLILPLYAICILIVEINKHKSTSNILNRRKATKFRELNDLVNSSSKSGINKKSLESQFEKFNLYHGSSND 515
[Close]
BLAST of SMED30030473 vs. Planmine SMEST
Match: SMESG000070513.1 (SMESG000070513.1)

HSP 1 Score: 247.669 bits (631), Expect = 4.530e-76
Identity = 133/213 (62.44%), Postives = 164/213 (77.00%), Query Frame = 1 
Query:  238 MNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKXXXXXXXXXXXXXXVTNFHKEITIMFETKREVIITEKDFTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNIIWLELMYICFVLPFYGMFFVILEIRKHKAVISIDKRRKATKYRNLNDLMRQCSRPLDNSQILQDKYGKLNLYQYSSSD 876
            MNFYCIMPFYPT GSVIIFAHNGYP DETYY L LF+NNEEVSFSSQ YI+IPY+ VG K+ LIG LLNLIN NLNVTN +KEI IMFET++EVII+ +DFTCADL+N E+ YHQLSK +L+FYAE+H L +   IW E + +  +LP Y +  +I+EI KHK+  +I  RRKATK+R LNDL+   S+   N + L+ ++ K NLY  SS+D
Sbjct:  408 MNFYCIMPFYPTRGSVIIFAHNGYPSDETYYTLSLFNNNEEVSFSSQQYIKIPYDTVGRKVVLIGKLLNLINPNLNVTNIYKEIWIMFETEKEVIISPRDFTCADLSNLEIRYHQLSKTTLLFYAEIHHLAIHYFIWTEFLCVLLILPLYAICILIVEINKHKSTSNILNRRKATKFRELNDLVNSSSKSGINKKSLESQFEKFNLYHGSSND 620
[Close]
BLAST of SMED30030473 vs. Planmine SMEST
Match: SMESG000070523.1 (SMESG000070523.1)

HSP 1 Score: 153.68 bits (387), Expect = 1.094e-42
Identity = 89/90 (98.89%), Postives = 90/90 (100.00%), Query Frame = 1 
Query:  232 VTMNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKXXXXXXXXXXXXXXVTNFHKEITIMF 501
            +TMNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKLIGSLLNLINSNLNVTNFHKEITIMF
Sbjct:  270 MTMNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKLIGSLLNLINSNLNVTNFHKEITIMF 359
[Close]
BLAST of SMED30030473 vs. Planmine SMEST
Match: SMESG000070531.1 (SMESG000070531.1)

HSP 1 Score: 98.2117 bits (243), Expect = 6.310e-22
Identity = 48/134 (35.82%), Postives = 80/134 (59.70%), Query Frame = 1 
Query:  241 NFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYIRIPYEVVGAKIKXXXXXXXXXXXXXXVTNFHKEITIMFETKREVIITEKDFTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNI 642
             F C+MPF+P PGS+IIFAHNGYPPD T Y + LF + EE+ F+  NYI++PY +   + ++ G++   +   +      +   + ++ ++ V IT+KD  C+  +  E++Y QLS  +L+F  +   L   N+
Sbjct:  532 TFVCVMPFFPIPGSIIIFAHNGYPPDLTTYAISLFLDGEEIGFTKVNYIKLPYLIEKRRFQIQGTIAFTLYFEIRNFTIQRSFFMEYDPEKVVTITKKDLECSQYSEIEMYYTQLSSFALVFVNDAFSLDSDNL 665
The following BLAST results are available for this feature:
BLAST of SMED30030473 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030473 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000070523.11.784e-14199.54SMESG000070523.1[more]
SMESG000070513.14.747e-7762.44SMESG000070513.1[more]
SMESG000070513.14.530e-7662.44SMESG000070513.1[more]
SMESG000070523.11.094e-4298.89SMESG000070523.1[more]
SMESG000070531.16.310e-2235.82SMESG000070531.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030473 ID=SMED30030473|Name=SMED30030473|organism=Schmidtea mediterranea sexual|type=transcript|length=1165bp
AAATAATTAAAATAAATAATTAAGATGATTAAATAAAACGGTATAATCAA
ATATCTGTTATTTAATGACTCTAGTCTTTATTGGCGACAAAGTGCGCTGG
AGTCCTTACTTCTTACTACTGGTAATCATGAAGTTTAGAACATTCATCAT
AATATTGTGGTTTTCTAATTTAAAATTTTTATATATTCAAAATTCTTTTA
AAATTGATTTTAATTTTATATTTCTCATTTAGTGACAATGAATTTTTATT
GCATAATGCCATTTTATCCGACTCCAGGTTCAGTGATAATATTCGCTCAT
AACGGATACCCCCCAGATGAAACTTATTACAAATTATTTTTATTTAGCAA
TAATGAAGAAGTTTCATTTTCATCTCAAAATTATATCAGAATCCCTTATG
AAGTAGTCGGGGCAAAAATTAAATTAATTGGATCATTACTAAATTTAATT
AATTCGAATTTGAATGTGACTAATTTTCACAAAGAAATTACGATAATGTT
CGAAACGAAAAGAGAAGTCATCATTACGGAGAAGGATTTCACCTGTGCTG
ATTTAACAAACGCGGAAGTACATTATCATCAGTTATCAAAAAACAGTCTC
ATCTTTTATGCTGAGCTGCATTTCCTTCGGGTTTCCAATATCATATGGTT
GGAACTGATGTACATATGTTTTGTTCTGCCTTTCTACGGAATGTTTTTTG
TTATCCTCGAAATAAGGAAACATAAAGCGGTGATATCTATTGACAAGAGG
AGAAAGGCTACTAAATACAGGAATCTGAATGACCTCATGCGTCAATGCTC
GCGACCATTGGACAATTCGCAAATCTTACAGGATAAATATGGAAAGCTTA
ATCTTTATCAATACAGCTCTAGTGACAAATAACTATTGATAATATTATGA
TTATATTTACTATTTTGATAATACTATTATTGACAAAGAAATTATTGACT
TAAATTAAGACTTATATTGGGCATTATGCTGTTCACTTTTTATTTGGTTT
TTTTCTGTTGAACACAGATTTTCAGCATTACATTTTTCAAGTATTCTTCA
ACAGTAGACAAATATGTACACTCCAAAAAAGACATGTTAGACAAGTGTTA
GACACTCCAAAAGACACGTGCTTTTGTATAACTAGTGCAAAACATATTAT
TTTATAGAAAAAAAA
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protein sequence of SMED30030473-orf-1

>SMED30030473-orf-1 ID=SMED30030473-orf-1|Name=SMED30030473-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=215bp
MNFYCIMPFYPTPGSVIIFAHNGYPPDETYYKLFLFSNNEEVSFSSQNYI
RIPYEVVGAKIKLIGSLLNLINSNLNVTNFHKEITIMFETKREVIITEKD
FTCADLTNAEVHYHQLSKNSLIFYAELHFLRVSNIIWLELMYICFVLPFY
GMFFVILEIRKHKAVISIDKRRKATKYRNLNDLMRQCSRPLDNSQILQDK
YGKLNLYQYSSSDK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 135..157